Regulation of gene expression plays a critical role in cellular differentiation and morphogenesis. Gene regulation requires multiple regulatory events, which involve the assembly of combinations of transcription factors (TFs) on cis-regulatory modules (CRMs). Pluripotent cells have a different gene expression profile than partially or fully differentiated cells and thus different regulatory events likely occur within pluripotent cells. Elucidation of the regulatory events that determine pluripotency as compared to partial or full differentiation of a cell may allow for production of pluripotent cells from differentiated cells. Thus, the deciphering of the “regulatory code” involved in directing pluripotency and differential gene expression profiles within a cell is the subject of intense research.
It is unclear whether a precise arrangement of TF binding sites (TFBSs) is necessary to execute a pluripotency regulatory event (Segal, E. and Widom, J. Trends Genet. (2009) 25(8): 335-43). In support for the hypothesis that TFBS placement is constrained, a composite motif has been identified that recruits a Sox2/Oct4 heterodimer to pluripotency CRMs as the core regulatory unit (Chen, X. et al., Cell (2008) 133: 1106-1117; Boyer, L. A. et al., Cell (2005) 122: 947-952; Loh, Y. H. et al., Nat. Genetics (2006) 38:431-40). It is possible that differently configured composite motifs recruit different Sox/Oct pairs that build the core of regulatory complexes in various cell types and for varying levels and types of cellular differentiation.
The Sox and POU (Oct) families of transcription factors consist of 20 and 14 members respectively, and often act synergistically during vertebrate development (reviewed in Bowles, J. et al., Dev. Biol. (2000) 227: 239-55; Ryan, A. K. & Rosenfield, M. G. Genes & Dev. (1997) 11: 1207-25; Wegner, M. Nucleic Acid Res (1999) 27: 1409-20). Despite their diverse biological roles the specificity of Sox proteins for DNA elements is largely indistinguishable and the amino acids involved in specific DNA contacts are highly conserved (Badis, G. et al. Science (2009) 324(5935):1720-3). Therefore, any single transcription factor may not be specific; rather, specificity in transcriptional control may instead be achieved as a result of selective heterodimerization. Indeed, several distinct Sox/POU pairs have been implicated as key regulators of cellular fates: Sox2/Oct4 are essential factors in (ES) cells (Boyer, L. A. et al., Cell (2005) 122: 947-952; Loh, Y. H. et al., Nat. Genetics (2006) 38:431-40; Rodda, D. J. et al. J Biol Chem (2005) 280:24731-7); Sox2/Brn2 was found important in neural development (Tanaka, S. et al. Mol Cell Biol (2004) 24: 8834-46); Sox11/Brn1 pair regulates glial cells (Kuhlbrodt, K. et al. J Biol Chem (1998) 273: 16050-7); and Sox17 has been shown to cooperate with Oct4 during mesendoderm formation (Stefanovic, S. et al. J Cell Biol (2009) 186: 665-73).